Background/Aims Biliary stone disease is one of the most common conditions leading to hospitalization. In addition to endoscopic retrograde cholangiopancreatography (ERCP), endoscopic ultrasonography (EUS) and magnetic resonance cholangiopancreatography (MRCP) are required in diagnosing choledocholithiasis. This study aimed to compare the sensitivity and specificity of EUS and MRCP against ERCP in diagnosing choledocholithiasis. Methods This retrospective study was conducted after prospective collection of data involving 62 suspected choledocholithiasis patients who underwent ERCP from June 2013 to August 2014. Patients were divided into two groups. The first group (31 patients) underwent EUS and the second group (31 patients) underwent MRCP. Then, ERCP was performed in both groups. Sensitivity, specificity, and diagnostic accuracy of EUS and MRCP were determined by comparing them to ERCP, which is the gold standard. Results The male to female ratio was 3:2. The mean ages were 47.25 years in the first group and 52.9 years in the second group. Sensitivity, specificity, accuracy, positive predictive value, and negative predictive value for EUS were 96%, 57%, 87%, 88%, and 80% respectively, and for MRCP were 81%, 40%, 68%, 74%, and 50%, respectively. Conclusions EUS is a better diagnostic tool than MRCP for diagnosing choledocholithiasis.